Biological analysis devices and systems

ABSTRACT

A biological analysis system can include an excitation module and an emission module. The excitation module can include a collimator element for receiving excitation light from the excitation light source and transmitting collimated excitation light in a first direction, and a plurality of excitation mirrors arrayed along the excitation light path, each excitation mirror disposed at an acute angle relative to the first direction and configured to reflect collimated excitation light along a second direction. The emission module can be positioned to receive excitation light transmitted along the second direction and can include a sample block comprising a plurality of sample receptacles positioned to receive a beam of collimated excitation light, and a plurality of photodetectors configured to receive emission light transmitted from a respective sample receptacle in a direction transverse to the second direction of the excitation light path.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to and the benefit of U.S. patentapplication No. 62/863,774, filed Jun. 19, 2019, the entirety of whichis incorporated herein by reference in its entirety for any and allpurposes.

FIELD OF INVENTION

The present invention relates to the analysis of biological samples.More particularly, the present application relates to apparatuses,systems, and methods for simultaneously analyzing a plurality ofbiological samples.

BACKGROUND

Fluorescence is the emission of light, often in the visible range, by acompound in response to its excitation by higher energy electromagneticradiation. As excited compounds return to a normal or baselineexcitation state, the excess energy is released in the form of light,typically at a less energetic wavelength than that used for excitation.In application, the emission light signals produced during fluorescencecan inform the identity and/or concentration of certain compounds withina sample. A fluorometer is one example of an analytical instrument thatuses excitation and emission spectra and intensities to analyzebiological samples. Using a fluorometer, the presence and concentrationof compounds, such as nucleic acid and some proteins, can be determined,whether outright or as part of of analysis workflows for DNA, RNA andproteins. Example applications include cloning, sequencing,transfection, qPCR, and protein assays.

In conventional fluorometers, ultraviolet excitation light is producedby an excitation light source (e.g., xenon lamp or mercury lamp) thatcan provide an intense and consistent source of radiation, therebyallowing saturation of the excitable compounds. The excitation light maybe collimated to improve excitation efficiency and then directed towarda biological sample of interest. Fluorescent samples, or fluorescingreagents bound to non-fluorescing samples, become activated throughexposure to the excitation light, causing the sample to fluoresce. Thisfluorescing emission light is received at a photodetector, and thesemeasurements of the amount, intensity, and/or distribution of light canbe used to identify and/or approximate concentrations of analyte withinthe sample.

Some fluorometers are configured to analyze a single sample at a time.The process of loading, taking measurements, and reloading samples is atime-consuming task for users needing to analyze and collect data onmany samples. In such cases, users trade the portability and lower costof single sample devices for an extremely low throughput. However,additional benefits are seen by performing single sample analysisincluding facilitating a reduction in excitation light pollution andnoise and easier analysis of the emission light. These advantages areachieved because of the singular nature of the optical system componentconfiguration. With only one sample being analyzed, there is only oneset of optical components needed to effectively excite and then captureand analyze the emission spectra from the sample. Stray reflections ofexcitation light and subsequent detection mixed with the desiredemission light can be minimized.

In contrast, for multi-sample devices, stray excitation light becomesmore difficult to mitigate as the number of samples increases. This isbecause as the number of samples increases, the configuration of theoptical system becomes more complex thus increasing the chances ofsample light paths interfering and causing cross-contamination ofemission light with excitation light. This cross contamination candecrease the effectiveness of activating fluorescent reagents and candistort the amount of light received by the photodetector, therebyskewing the corresponding measured concentrations of analyte included ineach sample.

There are inherent difficulties implementing multi-sample devices. Themost common commercial multi-sample format is the multiwell plate.Commercially available well plates typically have a standard geometricshape and size so they can be used across platforms (e.g., standardplates readers and centrifuges) without needing a bespoke machine oradaptor to facilitate use. Incidentally, the (essentially) predefinedvolume of the standard well plate affects the volume of sample that canbe processed in each well. Conventionally, the interior volume of theplate is divided into equally sized wells spaced equally apart fromnearest neighboring wells; 6-well, 12-well, 24-well, 48-well, 96-well,384-well, and 1536-well formats are commonplace.

Because the entire volume of the plate is conventionally divided intothe desired number of wells, the working volume for each well isinversely proportional to the total number of wells on the plate. Forexample, in a 6-well plate, the recommended working volume per well isbetween 3-5 mL, whereas in a 24-well plate, the recommended workingvolume per well is less—about 600 μL. In a similar fashion, 96-wellplates have a recommended working volume of 200 μL per well, with384-well and 1536-well plates having recommended working volumes of 80μL and 8 μL per well, respectively.

If a user opted to forego single sample fluorometry and instead wishedto conduct a multi-sample fluorometry assay, there is a dearth ofmulti-sample systems or formats that utilize a similarly small samplevolume as with the canonical single sample fluorometry systems. Instead,the user would be forced to use a multiwell plate having a sufficientlysmall working volume (e.g., a 96-well plate). While multiwell platesenable the automated, serial analysis of tens to hundreds of samples,most users use only a fraction of the available sampling wells foranalysis—thus rendering the high throughput as excessive. In instanceswhere sterile equipment is desirable, commonly accepted steriletechniques require the partially used plate to be discarded after theassay, and the large proportion of unused wells on discarded platestranslates to increased operating costs.

Furthermore, although multiwell plates can be analyzed usingcommercially available fluorometers configured to accept and processthese types of multi-sample plates, these systems are generally bulkierand more expensive than single sample fluorometers. Single samplefluorometers are also typically much smaller than their multiwell platereading counterparts, which can be several cubic feet in volume. Wherebench space in most laboratories is often limited, the footprint ofexperimental equipment is an important factor. Accordingly, a smallermulti-sample fluorometer is needed that can analyze multiple smallvolume samples without requiring specialized disposables (tubes, plates,etc.).

Accordingly, there are a number of problems and disadvantages in thefield of analyzing biological samples with optical systems. A need,therefore, exists to provide a biological analysis device, such as afluorometer, that can address at least some of the above problems.

BRIEF SUMMARY

Various embodiments disclosed herein are related to apparatuses,methods, and systems for an optical system configured for biologicalanalysis. Such embodiments beneficially improve optical systems,particularly in optical systems used in fluorometry devices, forexample, by enabling efficient multi-sample analysis.

A first aspect provides for a biological analysis system that includes(i) an excitation module and (ii) an emission module. The excitationmodule includes a collimator element configured to receive excitationlight from at least one excitation light source and to transmitcollimated excitation light along an excitation light path in a firstdirection, and a plurality of excitation mirrors arrayed along theexcitation light path, wherein each excitation mirror is disposed at anacute angle relative to the first direction and configured to reflect arespective beam of collimated excitation light along a second directionof the excitation light path. The emission module is positioned toreceive excitation light transmitted along the second direction of theexcitation light path, and the emission module includes a sample blockand a plurality of photodetectors. The sample block includes a pluralityof sample receptacles, each sample receptacle positioned to receive arespective beam of collimated excitation light transmitted along thesecond direction of the excitation light path, and each photodetector isconfigured to receive emission light transmitted in a third directionfrom a respective sample receptacle. In one aspect, the third directionis transverse to the second direction of the excitation light path.

In one aspect, the excitation module additionally includes a pluralityof excitation lenses arrayed such that each excitation lens ispositioned in the second direction of the excitation light path and isconfigured to focus a respective, reflected beam of collimated lightinto a respective focused beam of excitation light to be received at arespective sample receptacle of the emission module. In one aspect, eachphotodetector is oriented in the third direction toward the respectivesample receptacle. In one aspect, the third direction is substantiallyorthogonal to the second direction of the excitation light path.

In one aspect, the emission module additionally includes a plurality ofemission lenses configured to focus emission light transmitted in thethird direction onto the plurality of photodetectors. In one aspect, theemission module additionally includes a plurality of emission filterscorresponding to the plurality of emission lenses, the plurality ofemission filters being positioned downstream of the correspondingplurality of emission lenses and configured to allow emission light topass through the emission filter and to substantially block strayexcitation light. In one aspect, the plurality of emission filterscomprise dual bandpass filters. In one aspect, each emission lenscomprises a curved lens.

In one aspect, the emission module further comprises a plurality ofemission windows, each emission window associated with a respectivesample receptacle and defining an area through which emission light istransmitted to downstream components in the third direction.

In one aspect, at least one of the plurality of excitation mirrors isindependently adjustable.

In one aspect, the plurality of excitation mirrors are arrayed in astaggered, diagonal pattern formed by a first center point of a firstexcitation lens being offset vertically and horizontally from a secondcenter point of a second excitation lens, and the acute angle of eachexcitation mirror in the staggered, diagonal pattern is between 50° and75° relative to the first direction.

Embodiments of the present disclosure additionally include biologicalanalysis systems having (i) an excitation module and (ii) an emissionmodule. The excitation module includes an excitation light sourceconfigured to emit excitation light in a first direction; an excitationmirror selectively movable between a plurality of predefined positions,each predefined position forming an acute angles relative to the firstdirection and being configured to reflect the excitation light along asecond direction; and a plurality of excitation lenses arrayed such thateach excitation lens is positioned in the second direction and isconfigured to receive a reflected beam of excitation light directedthereto by the excitation mirror positioned in a respective predefinedposition. The emission module includes a plurality of sample receptaclespositioned to receive focused beams of reflected excitation light fromthe corresponding plurality of excitation lenses, and at least onephotodetector configured to receive emission light transmitted in athird direction from the plurality of sample receptacles. In one aspect,the third direction is transverse to the second direction.

In one aspect, the emission module additionally includes a plurality ofemission lenses and a plurality of emission filters configured to focusand filter the emission light onto the at least one photodetector. Inone aspect, the at least one photodetector includes a plurality ofphotodetectors, each photodetector configured to receive emission lightfrom a respective sample receptacle, the emission light having beenfocused and filtered by respective emission lenses and respectiveemission filters before being received at each photodetector.

In one aspect, the system additionally includes a sample loading systemconfigured to removably secure one or more sample containers withincorresponding sample receptacles of the plurality of sample receptacles.In one aspect, the sample loading system includes a closing mechanismconfigured to exert a closing force on—and to positionally secure—theone or more sample containers within the corresponding samplereceptacles.

In one aspect, the emission light comprises fluorescence radiation fromone or more excited fluorescent labels.

In one aspect, the system additionally includes a plurality of emissionapertures, wherein each emission aperture is associated with arespective emission lens of the plurality of emission lenses, andwherein each emission aperture is aligned in the third direction anddefines an area through which emission light is received from the samplereceptacle by the respective emission lens. In one aspect, a centerpoint of the emission aperture is aligned with an optical center of therespective emission lens.

Embodiments of the present disclosure additionally include biologicalanalysis systems having (i) at least two excitation light sourcesemitting different excitation wavelengths; (ii) a collimator elementconfigured to receive excitation light from the at least two excitationlight sources and to transmit collimated excitation light along anexcitation light path in a first direction; (iii) a plurality ofexcitation mirrors arrayed in a staggered, diagonal pattern along theexcitation light path, wherein each excitation mirror is disposed at anacute angle relative to the first direction and configured to reflect arespective beam of collimated excitation light along a second directionof the excitation light path; (iv) a plurality of excitation lensespositioned in the second direction of the excitation light path and isconfigured to focus respective, reflected beam of collimated light intocorresponding focused beams of excitation light; (v) a sample blockforming a plurality of sample receptacles, wherein the plurality ofsample receptacles are positioned to receive the corresponding focusedbeams of excitation light; and (vi) for each respective samplereceptacle, the biological analysis system includes at least thefollowing components aligned in a third direction, which in one aspectis transverse to the second direction: (a) an emission window definingan area through which emission light is transmitted in the thirddirection, (b) a curved lens configured to focus the emission lightpassing through the emission window, (c) a dual bandpass filter forsubstantially blocking stray excitation light, and (d) a photodetectorconfigured to receive the focused, filtered emission light.

This summary is provided to introduce a selection of concepts in asimplified form that are further described below in the detaileddescription. This summary is not intended to identify key features oressential features of the claimed subject matter, nor is it intended tobe used as an indication of the scope of the claimed subject matter.

Additional features and advantages of the disclosure will be set forthin the description which follows, and in part will be obvious from thedescription, or may be learned by the practice of the disclosure. Thefeatures and advantages of the disclosure may be realized and obtainedby means of the instruments and combinations particularly pointed out inthe appended claims. These and other features of the present disclosurewill become more fully apparent from the following description andappended claims or may be learned by the practice of the disclosure asset forth hereinafter.

BRIEF DESCRIPTION OF THE DRAWINGS

Embodiments of the invention will be better understood and readilyapparent to one of ordinary skill in the art from the following writtendescription, by way of example only, and in conjunction with thedrawings, in which:

FIG. 1 shows a schematic diagram of a biological analysis deviceaccording to an example embodiment.

FIG. 2 shows a schematic diagram of an excitation module of thebiological analysis device of FIG. 1 according to an example embodiment.

FIG. 3 shows a schematic diagram of an excitation module of thebiological analysis device of FIG. 1 according to another exampleembodiment.

FIGS. 4A and 4B show schematic diagrams of hypothetical opticalarrangements for comparison with the example embodiments.

FIG. 5 shows a schematic diagram of an excitation lens according to anexample embodiment.

FIG. 6 shows a partial cross-sectional view of the device of FIG. 1illustrating an operation of the excitation lens of FIG. 5.

FIG. 7 shows a partial cross-sectional view of the device of FIG. 1illustrating an emission module according to an example embodiment.

FIG. 8 shows a partial cross-sectional view of the device of FIG. 1illustrating a sample loading system according to an example embodiment.

FIG. 9 shows a schematic diagram of a biological analysis deviceaccording to another example embodiment.

FIG. 10 shows a schematic diagram of an example computer environmentincluding a computing system configured to implement methodscorresponding to the disclosed embodiments.

DETAILED DESCRIPTION

As used in the specification, a word appearing in the singularencompasses its plural counterpart, and a word appearing in the pluralencompasses its singular counterpart, unless implicitly or explicitlyunderstood or stated otherwise. Furthermore, it is understood that forany given component or embodiment described herein, any of the possiblecandidates or alternatives listed for that component may generally beused individually or in combination with one another, unless implicitlyor explicitly understood or stated otherwise. Additionally, it will beunderstood that any list of such candidates or alternatives is merelyillustrative, not limiting, unless implicitly or explicitly understoodor stated otherwise. In addition, unless otherwise indicated, numbersexpressing quantities, constituents, distances, or other measurementsused in the specification and claims are to be understood as beingmodified by the term “about.”

Accordingly, unless indicated to the contrary, the numerical parametersset forth in the specification and attached claims are approximationsthat may vary depending upon the desired properties sought to beobtained by the subject matter presented herein. At the very least, andnot as an attempt to limit the application of the doctrine ofequivalents to the scope of the claims, each numerical parameter shouldat least be construed in light of the number of reported significantdigits and by applying ordinary rounding techniques. Notwithstandingthat the numerical ranges and parameters setting forth the broad scopeof the subject matter presented herein are approximations, the numericalvalues set forth in the specific examples are reported as precisely aspossible. Any numerical values, however, inherently contain certainerrors necessarily resulting from the standard deviation found in theirrespective testing measurements.

Furthermore, as used in the specification and appended claims,directional terms, such as “top,” “bottom,” “left,” “right,” “up,”“down,” “upper,” “lower,” “proximal,” “adjacent,” “distal,” and the likeare used herein solely to indicate relative directions and are nototherwise intended to limit the scope of the specification or claims.

As described above, single sample fluorometry devices allow for a smallfootprint, low disposable waste, and are usually easier to configure forprecise, accurate measurements. However, due to the low throughput, thetime necessary to analyze multiple samples in sequential order becomesincreasingly longer as more samples are measured. Because of this, manyusers opt for multiwell plate readers configured for fluorometry.However, these devices are large, expensive, produce more disposablewaste, and require external mitigation (i.e., specialized plates withlight impermeable well walls) to ensure accurate, precise datameasurements. Further, as verified in user surveys, there is anoutstanding need in the market for a fluorometer that can analyze morethan one sample at a time without requiring the high volumes associatedwith multiwell sample plates.

The embodiments provided herein overcome one or more of the notedproblems in the art and are directed to a biological analysis system forsimultaneously analyzing multiple samples. For example, the systemdisclosed herein include a uniquely designed excitation module andcorresponding emission module that significantly decreases the footprinttypically associated with multi-sample fluorometers. Furthermore,components of the disclosed optical systems can be independently tunableto accommodate various and variable configurations of sample loadingsystems, such as a different number of sample wells or the orientationof the sample wells in relation to each other. Additionally, thedisclosed systems are designed to reduce the amount of stray excitationlight observed by sample sensor(s) and can prevent cross-contaminationof light between samples—all while maintaining a small footprint andwithout requiring specialized disposable products. Indeed, the disclosedsystems can receive and analyze biological samples using the same samplecontainers as conventional single sample fluorometers (e.g., 500 μLthin-walled polypropylene tubes).

FIG. 1 shows a schematic diagram of a biological analysis system 100according to an exemplary embodiment. The biological analysis system 100of FIG. 1 is depicted as a fluorometer having an optical system thatincludes an excitation module 102 and an emission module 104. Theexcitation module 102 excites one or more samples (or fluorescent tagswithin samples) to generate emission light, and the emission module 104detects the emission light for analysis.

The excitation module 102 includes one or more excitation light sources(e.g., LED 106 and/or LED 108), a beam splitter 110 configured to directone or more beams of excitation light generated by the light source(s)in a first direction (e.g., direction 114A) a collimator element 112, aplurality of excitation mirrors 116 configured to direct one or morebeams of excitation light in a second direction (e.g., direction 114B)toward a plurality of excitation lenses 118 and a plurality of samplereceptacles 120 configured to receive sample containers whose excitedcontents produce emission radiation in a third direction (e.g.,direction 114C) toward a plurality of emission lenses 122, a pluralityof emission filters 124, and a plurality of photodetectors 126.

The excitation module 102 can utilize a plurality of excitation lightsources, such as the blue light emitting diode (LED) 106 and red LED 108illustrated in FIG. 1, but it will be appreciated that other types ornumber of excitation light sources, including various excitationwavelengths, may be used. Additional, or alternative excitation lightsources include, for example, lasers or mercury/xenon arc lamps. Theexcitation light source can include be selected based on wavelengthranges associated with violet, green, yellow, or orange visible lightspectra, and/or non-visible light ranges, such as ultraviolet, nearinfrared, or infrared lights. In some embodiments, one or moreexcitation light sources used in the excitation module is selected basedon the anticipated identity of analyte to be analyzed within abiological sample.

In some embodiments, the excitation light sources (e.g., LED 106, 108)are specifically tuned to the excitation wavelengths of pre-determinedfluorophores. In the illustrated example of FIG. 1, the wavelengths ofexcitation light produced by the blue LED 106 and the red LED 108,respectively, are selected based on the excitation wavelength of knownfluorophores to be used in the analysis of biological samples.Alternatively, a high intensity light source, such as a xenon/mercuryarc lamp can be used be used as an excitation light source. Such lampsgenerate both ultraviolet (UV) light and visible light, making theirimplementation more practical for non-specific analyses where the exactexcitation wavelength or range of wavelengths is unknown. A light sourceproducing a single excitation wavelength or known range of excitationwavelengths can beneficially target a known fluorophore and therebyprevent or reduce inadvertent excitation of non-targeted moleculeswithin the sample. In some embodiments, an excitation filter (e.g., abandpass filter) can be disposed in front of the excitation light sourcenarrow the wavelength range of the excitation light, as desired.

As shown in FIG. 1, a beam splitter 110 is used to direct the two beamsof excitation light from LEDs 106, 108 along the same light path (e.g.,direction 114A), thereby reducing the number of components and spaceused by the excitation module 102. Alternatively, an optical fiber beamcombiner, or the like, may be used in place of the beam splitter 110.This illustrated configuration is highly beneficial because theexcitation module size is reduced, making the overall footprint of thecorresponding biological analysis device to also be reduced.Furthermore, the ability to include one or more excitation light sourcesallows for increased versatility and bespoke configurations of thesystem for analyzing different samples and/or various types offluorophores, which may correspond to different ranges of excitationlight.

The excitation light, after passing the beam splitter 110, is collimatedthrough a collimator element 112 (e.g., a collimator lens or aconcave/parabolic mirror). The collimated beam of excitation light istransmitted along a first direction 114A toward a plurality ofexcitation mirrors 116. The first direction 114A is generally parallelto the optical axis of the collimator element 112. The excitation lightis reflected from the mirrors 116 in the form of a plurality ofseparate, reflected beams toward a corresponding plurality of excitationlenses 118. Each excitation lens 118 focuses a corresponding reflectedbeam of excitation light, generating focused beams (e.g. line-focalbeams) to illuminate the samples received within the sample receptacles120 of the emission module 104. The fluorophore(s) within each sampleare excited by the focused beams of excitation light and generateemission light.

As shown in FIG. 1, the separate, reflected beams of excitation lightare reflected from each corresponding excitation mirror and travel in asecond direction (e.g., direction 114B). In some embodiments, the seconddirection is non-perpendicular relative to the first direction and formsan acute angle with the first direction, thereby causing the reflectedbeams of excitation light to travel in a direction back toward thecollimator element 112. In contrast, some conventional fluorometeroptical systems are configured to direct the light path downward,perpendicular to the light path, thus increasing the length of theoverall optical system as compared to that provided by the illustratedstaggered mirror configuration. Additionally, some conventionalfluorometer optical systems do not include reflection excitation mirrorsallowing the collimated light to continue on its initial trajectorybefore passing through any filters and reaching the targeted samples.Such embodiments result in a much larger system than that illustrated inFIG. 1. Therefore, the staggered mirror configuration as shown anddescribed in FIG. 1 beneficially reduces the size of the optical system.

As alluded to above, the plurality of excitation lenses 118 generatefocused beams of excitation light that travel from the excitation module102 to the emission module 104. The emission module 104 includes aseries of biological sample receptacles 120 formed into a sample block.As shown, the plurality of sample receptacles 120 are arranged as aseries of uniformly spaced receptacles aligned along an axis that isapproximately parallel to the first direction 114A of collimated light.

Each receptacle 120 is associated with a respective emission lens 122,emission filter 124, and photodetector 126 (e.g. photodiodes,photomultiplier tubes, CCD/CMOS sensors, etc.). The emission module 104is configured relative to the excitation module 102 such that eachfocused beam of excitation light generated by the excitation module 102travels to—and excites the contents of—a single sample containerarranged within a sample receptacle 120 of the emission module 104.

Emission light (e.g., emission radiation, fluorescence radiation)emitted by fluorescing labels or molecules within samples housed inreceptacles 120 is collected by individual emission lenses of theplurality of emission lenses 122, ensuring that cross-contamination ofemission light from adjacent or multiple samples is prevented orminimized by focusing the emission light along the third direction 114Ctoward respective photodetectors. The focused emission light then passesthrough a respective emission filter of the plurality of emissionfilters 124 to be subsequently detected by respective photodetectors126. In some embodiments, each photodetector 126 is beneficiallydisposed at a distance determined by a focal length of the correspondingemission lens 122, so that the emission light beam passing through theemission lens reaches the target photodetector when it is optimallyfocused to a line-beam. This is beneficial in case one or more of thecomponents are misaligned slightly by ensuring that the emission lightreaches at least a portion of the surface of the photodetector lens.

As facilitated by the configuration of the optical components of theexcitation module 102 and emission module 104, the emission light isbeneficially obtained in a different direction than the excitationlight. It is desirable to obtain the emission light in a directionincident to the excitation light so as to avoid receiving directexcitation light at the emission light sensor (e.g., photodetector 126).Emission radiation is emitted in all directions from the excited sample,and most of the excitation light remains directed in the seconddirection 114B. By placing the emission optics in a direction transverse(e.g., orthogonal) to the second direction 114, much of the emissionlight can be observed in the absence of most of the excitation light.Any low-level excitation light reflected in the third direction can befiltered out by emission filters 124 (e.g., bandpass filters) beforereaching the photodetector 126.

As discussed above, embodiments of the present disclosure include anexcitation module 102 having a plurality of excitation mirrors 116 thatreflect collimated excitation light at an acute angle towards aplurality of excitation lenses 118. FIGS. 2 and 3 show variousalternative embodiments of the excitation module 102 of the biologicalanalysis system 100 of FIG. 1. In such embodiments, each of theexcitation mirrors (e.g., excitation mirrors 202 a-202 h and/or 302a-302 h) is disposed at an acute angle relative to the direction of thecollimated excitation light transmitted from the collimator element 212.For example, in FIG. 2, the plurality of mirrors 202 a-202 h is disposedat an angle of approximately 45° relative to the direction 204 of thecollimated excitation light. Accordingly, the reflected beams ofexcitation light in FIG. 2 are approximately perpendicular to theincident beam (i.e., the collimated excitation light). Accordingly, insuch embodiments, the plurality of sample containers 226 a-226 h (wheresample container 226 a corresponds to excitation mirror 202 a, samplecontainer 226 b corresponds to excitation mirror 202 b, and so on) aredisposed along a uniform axis at intervals that position each samplecontainer in the path of each reflected beam of excitation lightreflected from each excitation mirror.

In FIG. 3, the plurality of mirrors 302 a-302 h are disposed at an angleof approximately 67.5° relative to the direction 304 of the collimatedexcitation light (i.e. the collimated excitation light is approximately22.5° to a direction normal to the mirrors 302 a-302 h). Accordingly,the reflected beams of excitation light in the embodiment of FIG. 3 areapproximately 45° to the incident beam (i.e., the collimated excitationlight). Thus, the reflected beams of excitation light travel in a seconddirection (also see, second direction 114B of FIG. 1) from thecollimated excitation light, which is generally parallel to the opticalaxis of the collimator 312.

FIG. 3 also shows the optical system including a plurality of excitationlenses 318 a-318 h corresponding to the plurality of excitation mirrors302 a-302 h. For example, excitation mirror 302 a corresponds toexcitation lens 318 a, excitation mirror 302 b corresponds to excitationlens 318 b, and so on. As shown, each excitation lens 318 a-318 h isdisposed at an angle such that the reflected beams of excitation lightreflected from each excitation mirror 302 a-302 h is approximatelyparallel with (and aligned with) the optical axis of the excitationlenses 318 a-318 h.

In some embodiments, at least one of the excitation mirrors 202 a-202 hand 303 a-302 h is independently adjustable to compensate for anyoptical errors by the collimator or positioning errors of the lightsource or beam splitter. For example, mirrors 202 a and 202 h may bepositioned at a slightly different angle compared to mirrors 202 b-202g, as the beam of excitation light transmitted by the collimator may beless collimated at the outer edges compared to the center.

It should be appreciated that while each of the examples in FIGS. 2-3depict eight excitation mirrors and eight corresponding excitationlenses, the number of mirrors and lenses may be different in alternateembodiments, depending on the design of the overall optical system andits excitation and emission components, on the number of samples to besimultaneously analyzed by the biological analysis system 100, or onother factors. For example, a similar device configured to analyze up totwenty samples simultaneously could employ twenty sets of mirrors andlenses can address the needs of user with higher sample multiplexingrequirements while still providing the benefits described herein such asreducing the overall size and footprint of the device. In anotherexample, a similar device can be configured to analyze up to twelvesamples wherein the excitation module could then be adjusted by wideningthe collimation beam to ensure coverage of the additional samples.Alternatively, additional optics could be used to split the collimatedbeam into one or more sub-beams while maintaining sufficient beamintensity for the desired application.

As described above, many conventional multi-sample devices have verylarge footprints that are the result of the associated configuration ofoptical components and corresponding sample loading system. For example,referring now to FIG. 4A, when the sample containers (e.g., samplecontainers 426 a-426 h) are configured to receive microcentrifuge tubes(or similar), and the tube to tube distance (i.e., distance betweenadjacent samples) is 9 mm, the entire length (e.g., length 402) of thecorresponding sample container strip of 8 tubes is about 70 mm. If thecollimated excitation beam is to directly illuminate the strip of 8tubes, the size (e.g., length 402) of the collimated beam needs to belarger than 70 mm. Hence the collimator and associated optics and therequired space would be quite large, as illustrated in FIG. 4A.

Similarly, if a single excitation mirror (or a plurality of excitationmirrors aligned along a similar axis shown by the single excitationmirror) is to be placed at an angle of 45° to the collimated beam toreflect the excitation light to the strip of 8 tubes, the collimator andassociated optics and the required space would still be large, asillustrated in FIG. 4B. The increased space required is furtheremphasized when considering the separation of the excitation light beamsand the emission radiation (i.e., the angles at which each stage oflight is traveling should be non-parallel to facilitate a reduction instray excitation light being received by a photodetector). Strayexcitation light will adversely affect the ability of a photodetector toaccurately detect a precise amount of emission radiation and thereforecan skew the concentration calculations corresponding to a biologicalsample. Thus, in such instances, any subsequent optical components willbe positioned accordingly, thereby increasing the width and/or length ofthe optical system and thus the overall biological analysis device whichhouses the optical system.

In contrast, the optical systems of the present disclosure utilize aplurality of individual mirrors (e.g., 8 mirrors in the non-limitingexamples depicted in FIGS. 1-3) in a staggered arrangement (i.e., eachmirror is laterally offset from an adjacent mirror) along a diagonalaxis to fold the light path, as shown in FIGS. 2-3.

For example, with reference to FIG. 3, if the angle of the mirrors 302a-303 h relative to the direction 304 of the collimated excitation lightis 67.5°, the reflected beams from the mirrors 302 a-302 h traveldownward (i.e., in a direction away from the excitation mirrors 302a-302 h and toward the excitation lenses 318 a-318 h) and leftward (in adirection opposite to the direction of the excitation light path flowingfrom the collimator 312). In FIG. 3, if the vertical center-to-centerdistance between adjacent mirrors is 2.772 mm, and the horizontalcenter-to-center distance between adjacent mirrors is 6.228 mm, then thehorizontal center-to-center distance of adjacent reflected beams is 9mm, which is the tube-to-tube distance. With such an arrangement, thewidth of the collimated beam of excitation light will only be about2.772 mm×8≈22.2 mm, which is much smaller than the above 70 mm. Due to“Z” layout (see light directions 114A-114C of FIG. 1), the overalloptics are also compact. In one embodiment, this can allow for anoverall size reduction of more than 80% compared to the arrangementillustrated in FIG. 4A.

With continued reference to FIGS. 2-3, the acute angle at which eachexcitation mirror is disposed can be between about 50° and 75° to formthe “Z” layout. If, for example, the angle is close to 90°, the anglebetween the incident and reflected beams from the mirrors is close to0°, then all mirrors will be positioned much further away from thecollimator (e.g., collimators 212, 312) to ensure that the excitationlenses (e.g., excitation lenses 318 a-318 h) as well as the emissionmodule can be placed outside the collimated beam. On the other hand, ifthe angle is close to 45°, e.g., close to the arrangement in FIG. 2, itis difficult to both accommodate the emission module in the tube stripdirection because of very limited space from tube to tube while alsoensuring that the angle between the direction of excitation beam andemission detection is 90° degrees to minimize the amount of excitationlight in the direction of emission detection, which helps to reducebackground signal and increase detection sensitivity.

The path of the excitation light from collimator element 212 to theexcitation mirrors into a plurality of reflected beams follows theprinciples corresponding to the law of reflection. For example, theangle of incidence (i.e., the angle at which the collimated light hitsan excitation light) equal the angle of reflection (i.e., the angle atwhich the excitation light is reflected towards the sample containers).Additionally, the angle of incidence is, in part, based on the directionof the collimated light (e.g., direction 204 and/or first direction114A) which is fixed. When the position of a sample container isdetermined, the horizontal (“x”) distance and vertical (“y”) distancefrom the excitation mirror (e.g., a center point of the excitationmirror) is known. It should be appreciated that the acute angle at whichthe excitation mirror is disposed is equal to the angle of incidence ofthe collimated excitation light based from geometric principles ofcongruent interior angles between one or more parallel lines. Assumingthat the rotation of the excitation mirror negligibly affects the knownx and y distances between the excitation mirror and the samplecontainer, the acute angle (θ_(m)) at which to rotate the excitationmirror is approximately based on the following equation:

$\theta_{m} = {\frac{{180{^\circ}} - {{ArcTan}\left( \frac{y}{x} \right)}}{2}.}$

It therefore follows that the amount by which a subsequent excitationmirror corresponding to a subsequent sample container to be analyzedshould be offset from the previous excitation mirror is proportional tothe amount by which the subsequent sample container is offset,vertically and/or horizontally, from a previous sample container. Thehorizontal and vertical offsets then characterize the pattern of thestaggered, diagonal configuration of the excitation mirrors.

Alternatively, because the exact angles and offsets of the mirrors canbe calculated precisely, a single excitation mirror may be used—insteadof the staggered array—which is able to rotate through a range ofcorresponding incident and reflection angles such that the direction ofthe reflected excitation light (i.e., second direction 114B) is directedto individual excitation lenses and/or sample receptacles serially overshort intervals of time. While embodiments of the biological analysissystem that include a plurality of excitation mirrors allow for eachbiological sample to be analyzed simultaneously, the single, movablemirror embodiments cannot simultaneously analyze each sample. However,the reduction in overall analysis time can be negligible given the smallnumber of samples analyzed.

The excitation lenses can focus a beam of excitation light of any shapeinto a line-focal beam. FIG. 5 shows a schematic diagram of anexcitation lens 500 suitable for use as one of the excitation lenses 118in the system 100 of FIG. 1 according to an example embodiment, and FIG.6 shows a partial cross-sectional view of the system 100 of FIG. 1illustrating an operation of the excitation lens 500 of FIG. 5.

In the illustrated example, the excitation lens 500 is a cylindricallens that can substantially reduce the beam width in one direction,while maintaining the beam width in another direction. In other words,the excitation lens 500 can manipulate an incoming beam such that afocal line is produced, instead of a focal beam. Referring now to FIG.6, for example, when the excitation lens 600 (e.g., excitation lens 500of FIG. 1) is mounted vertically, the excitation lens 600 can focus abeam of excitation light into a horizontal line-focal beam 604, as shownin FIG. 6. Due to the line-focal beam, the interaction volume betweenexcitation beam and liquid sample inside the sample container 602 isless sensitive to tolerance and assembly error. In other words, even ifthe sample container 602 is slightly offset from its normal or intendedposition, the line-focal beam 604 can still effectively excite thesample contained in the sample container 602. In systems capable ofanalyzing multiple fluorophores, such as the system 100 of FIG. 1, thefocal lengths of the different excitation lenses are independentlyselectable, such that the focal lengths may be different from channel tochannel in order to improve signal balancing across channels.

In some embodiments, as illustrated, the line-focal beam 604 passesthrough an excitation window 606 which facilitates a reduction in strayexcitation light, for example, excitation light corresponding to one ormore other excitation mirrors and/or lenses. In some instances, theexcitation window is defined by an opening in a receptacle (e.g.,receptacle 804 of FIG. 8). In some instances, the excitation window 606is formed integrally with internal components of a sample loading system(e.g., sample loading system 800 of FIG. 8). In some instances, theexcitation window 606 is an attachment component (e.g., an adjustableaperture diaphragm) disposed between the excitation lens 600 and thesample container 602.

After passing through the excitation window 606 and traveling in asecond direction (e.g., second direction 114B of FIG. 1), the excitationlight illuminates the biological sample (i.e., contents of the samplecontainer within the respective receptacle). In some embodiments, theline-focal beam 604 of excitation light hits a barrier wall (e.g., wall608) configured to absorb light and/or prevent stray excitation lightfrom traveling outside the sample container 602.

FIG. 7 shows a partial cross-sectional view of the system 100 of FIG. 1illustrating an emission module 700 suitable for use as the emissionmodule 104 according to an example embodiment. The emission module 700includes multiple sets of optical elements, including: an emissionwindow 710 formed by an emission flange 720, an emission lens 702, anemission filter 704, and a photodetector 706. Fluorescence radiationemitted by an excited fluorophore is allowed to pass through theemission window 710 and is transmitted from the sample receptacle 712through the transparent area that is restrictively defined by theemission window 710. In some instances, the emission window 710 isdefined by an opening in a receptacle (e.g., receptacle 804 of FIG. 8)configured to removably secure the sample container. In some instances,the emission window 710 is formed integrally with internal components ofa sample loading system (e.g., sample loading system 800 of FIG. 8). Insome instances, the emission window 710 is an attachment component(e.g., an adjustable aperture diaphragm) disposed between the emissionlens 702 and the sample receptacle 712. In some embodiments, theemission module 700 does not include an emission window 710.

In some embodiments, each sample receptacle 120 is beneficially disposedat approximately a distance determined by a focal length of thecorresponding excitation lens 118. Alternatively, each sample receptacle120 is disposed such that it receives a width and/or height associatedwith the focused beam of excitation light, wherein the width and/orheight corresponding to a width and/or height of an excitation window.

After passing through the emission window 710, the emission radiation isfocused by the emission lens 702 to improve signal-to-noise ratio. Thefocused fluorescence radiation then passes through the emission filter704 which can block stray light transmitted by the emission lens 702. Inone implementation, the emission filter 704 is in the form of first dualbandpass filter 704 a and second dual bandpass filter 704 b, which areconfigured to block radiation corresponding to the excitation light. Theuse of dual bandpass filters 704 a, 704 b can provide blocking of lightof selected wavelength ranges in a compact configuration. For example,if the excitation light is generated by red or blue LEDs, each of thedual bandpass filters 704 a, 704 b can block red and blue lights tominimize stray excitation light.

In some embodiments, the emission lens 702 is fitted with an emissionflange 720 configured to prevent stray excitation light and/or undesiredemission radiation from a non-corresponding sample container fromreaching the photodetector 706. For example, as illustrated in FIG. 7,an emission flange 720 can form an emission aperture configured todefine an area through which emission radiation generated by onebiological sample housed in the sample receptacle 712 is allowed to passthrough to reach the emission lens 702. In some instances, the emissionaperture functions as the emission window 710 (i.e., there is nostandalone or embedded emission window). The emission flange 720 canalso include a circumferential side wall 724 configured to surround thecorresponding emission lens 702, wherein the circumferential side wallextends past a thickness of the emission lens 702. The side wall 724 (ormultiple side walls) of the emission flange 720 extend in the thirddirection (e.g., third direction 114C of FIG. 1) toward the emissionfilters 704 a, 704 b and/or the photodetector 706 and can form a channelprotecting the emission lens from receiving stray light.

In some embodiments, the emission flange 720 is beneficially disposedsuch that the center point of the emission aperture/window is alignedwith an axis line defined by the optical center of the emission lens 702and the optical center of the photodetector 706. In some instances, theemission flange 720 is disposed at an angle wherein the outer surface ofthe end of the emission flange 720 forming the emission aperture isflush with an outer surface of the sample receptacle 712 and/or emissionwindow 710. In some embodiments, the circumferential (e.g., cylindrical)side wall 724 of the emission flange 720 extends until it meets theouter circumference of the emission filter 704 and/or one or more of thedual bandpass filters (704 a, 704 b) of the emission filter 704 in orderto create an enclosed space through which the emission radiation cantravel shielded from stray excitation light and/or emission radiationfrom a neighboring sample container.

In some embodiments, the sample receptacle 712 is disposed such thatemission radiation is limited to being transmitted through the emissionwindow 710, wherein the emission radiation path is blocked by anemission wall 708 disposed on the opposite side of the emission window710. In this manner, the photodetector 706 “sees” emission radiationtraveling through the aforementioned openings from the sample receptacle712. In some embodiments, the emission wall 708 is an integratedcomponent in the emission module 700.

The biological analysis system 100 according to the example embodimentsalso includes a sample loading system adapted for a multiple-sampleenvironment. FIG. 8 shows a partial cross-sectional view of an exemplarysample loading system 800 (e.g., that can be adapted for use with system100 of FIG. 1). The sample loading system 800 includes a sample block802 which has a plurality of receptacles 804. The receptacles 804 canreceive a corresponding plurality of sample containers 806, with eachsample container 806 containing a respective sample. In a non-limitingexample, eight receptacles are disposed in a single straight row toreceive a strip of eight sample containers. It will be appreciated thatin other embodiments, the receptacles may be arranged in a differentfashion, e.g. alternating or wave-like (see FIG. 9). Also, the number ofreceptacles may be varied depending on the number of samples to besimultaneously analyzed.

Each receptacle 804 is also designed to positionally secure therespective received sample container 806. As shown in FIG. 8, a bottomsurface of each receptacle 804 includes a depression 808 which isconfigured to receive a bottom tip portion 810 of the respective samplecontainer 806. In addition, a receptacle opening 812 of each receptacle804 is fitted with a gasket 814 (which is also representative of gasket714 of FIG. 7), which engages with a cap 818 of the respective samplecontainer 806. Gasket 814 may comprise any suitable material, e.g.,rubber, silicone. When a sample container 806 is fully inserted into thereceptacle 804, the sample container 806 is effectively held in place bythe depression 808 and gasket 814, with the wall of the sample container806 not touching the wall of the receptacle 804.

The sample loading system 800 also includes a closing mechanism 816capable of exerting a closing force on the plurality of samplecontainers 806. In one implementation, the closing mechanism 816 isconfigured to press on caps 818 of the plurality of sample containers806. For example, the closing mechanism 816 includes a plurality ofbiasing members, e.g. springs 820, which can operate independently ofone another. In use, if one cap 818 is not fully closed, a correspondingspring 820 can act on the cap 818 to depress it, to prevent adjacentsample containers from being positionally displaced. The springs 820also help to further secure the sample containers 806 in the verticaldirection. In an alternate implementation, the closing mechanism 816 mayinclude sealing members configured to close the sample containers 806when the closing mechanism 816 acts on the sample containers 806.Further, alternate forms of biasing members include bellow-likestructures made of an elastic material such as rubber.

As described above with reference to FIG. 1, some embodiments of theoptical system of the biological analysis system include a plurality ofmirrors, uniformly spaced and uniformly angled in relation to oneanother. However, it is anticipated that, in some embodiments, eachexcitation mirror of the plurality of excitation mirrors isindependently adjustable to accommodate for variable configurations andsizes of sample containers. Therefore, by adjusting one or moreexcitation mirrors of the optical system, the biological analysis deviceis able to facilitate the measurement of a diversity of samplecontainers to be read simultaneously.

Referring now to FIG. 9, an example embodiment of the biologicalanalysis system 100 of FIG. 1 is provided, wherein similar componentsare shown and wherein an alternate configuration of the plurality ofexcitation mirrors 916 and sample receptacles 920 are shown. Asillustrated, the plurality of sample receptacles 920 is disposed in astaggered, alternating pattern. In some embodiments, the staggered,alternating pattern forms one or more rows of sample receptaclesdisposed with a vertical and/or horizontal offset from each other.Accordingly, the plurality of excitation mirrors 916 are configured suchthat the optical path of excitation light from the collimator element912 reaches each of the sample containers of the plurality of samplereceptacles 920 as discrete beams of focused excitation light. Asillustrated, the plurality of excitation mirrors is disposed in astaggered, alternating pattern along a diagonal axis. In someembodiments, the staggered, alternating pattern forms one or more rows(i.e., excitation mirrors disposed along one or more parallel diagonalaxes, the axes disposed at an acute angle to the direction of collimatedlight. Each excitation mirror 916 is disposed at a vertical and/orhorizontal offset from one or more proximate excitation mirrors 916. Itshould be appreciated that the staggered pattern of the excitationmirrors of FIG. 1, FIG. 9, and/or an alternative embodiment are formedin a plurality of different configurations to accommodate variations insample container configurations.

While FIG. 9 depicts an alternative embodiment of sample loading systemand corresponding configuration of excitation mirrors, other opticalsystem configurations are possible, including the addition or omissionof certain optical components. For example, in some embodiments, theoptical system may include a 1:1:1:1 ratio between the excitationmirrors, excitation lenses, emission filters, and photodetectors (e.g.,FIGS. 1 and 9). In some embodiments, a single emission filter and asingle detector array are used without the integration of excitationmirrors or excitation lenses. Alternatively, in some embodiments, ascanning detection head including an emission lens, an optical emissionsfilters, and photodetector is used to scan across the samples.

As described above, disclosed embodiments directed to the biologicalanalysis device include a novel configuration of an optical systemachieving many benefits over conventional multi-sample fluorometers. Inaddition to an optical system and sample loading system, the device mayalso be configured as a computerized device. For example, referring nowto FIG. 10, a computing environment 1000 incorporating a biologicalanalysis device, for example system 100 of FIG. 1 and/or system 900 ofFIG. 9, is illustrated. In some embodiments, the biological analysissystem 1100 includes the optical system as described above and/or acomputing system 1200. As shown, the computing system 1200 includes oneor more processors 1240 and one or more hardware storage devices 1220that store computer-executable instructions (e.g., instructions1220A-1220D) that are executable by the one or more processors to causethe computing system 1200 to perform various acts corresponding to thedisclosed embodiments herein. In some embodiments, the computing system1200 facilitates the inclusion of a user-interface 1300 a of thebiological analysis system 1100.

Embodiments disclosed or envisioned herein may comprise or utilize aspecial purpose or general-purpose computer (e.g., computing system1200) including computer hardware, such as, for example, one or moreprocessors, as discussed in greater detail below. Embodiments may alsoinclude physical and other computer-readable media for carrying orstoring computer-executable instructions and/or data structures. Suchcomputer-readable media can be any available media that can be accessedby a general purpose or special purpose computer system.Computer-readable media that store computer-executable instructions(e.g., instruction 1220A-1220D) are physical storage media.Computer-readable media that carry computer-executable instructions aretransmission media. Thus, by way of example, and not limitation,embodiments can comprise at least two distinctly different kinds ofcomputer-readable media: computer storage media (e.g., hardware storagedevice 1220) and transmission media.

Computer storage media includes RAM, ROM, EEPROM, CD-ROM or otheroptical disk storage, magnetic disk storage or other magnetic storagedevices, or any other medium which can be used to store desired programcode means in the form of computer-executable instructions or datastructures and which can be accessed by a general purpose or specialpurpose computer.

A “network” (e.g., network 1500) is defined as one or more data linksthat enable the transport of electronic data between computer systemsand/or modules and/or other electronic devices. When information istransferred or provided over a network or another communicationsconnection (either hardwired, wireless, or a combination of hardwiredand wireless) to a computer, the computer properly views the connectionas a transmission medium. Transmission media can include a networkand/or data links which can be used to carry data or desired programcode means in the form of computer-executable instructions or datastructures and which can be accessed by a general purpose or specialpurpose computer. Combinations of the above should also be includedwithin the scope of computer-readable media.

Further, upon reaching various computer system components, program codemeans in the form of computer-executable instructions or data structurescan be transferred automatically from transmission media to computerstorage media (or vice versa). For example, computer-executableinstructions or data structures received over a network or data link canbe buffered in RAM within a network interface module (e.g., an “NIC”),and then eventually transferred to computer system RAM and/or to lessvolatile computer storage media at a computer system. Thus, it should beunderstood that computer storage media can be included in computersystem components that also (or even primarily) utilize transmissionmedia.

Computer-executable instructions comprise, for example, instructions anddata which cause a general-purpose computer, special purpose computer,or special purpose processing device to perform a certain function orgroup of functions. The computer executable instructions may be, forexample, binaries, intermediate format instructions such as assemblylanguage, or even source code. Although the subject matter has beendescribed in language specific to structural features and/ormethodological acts, it is to be understood that the subject matterdefined in the appended claims is not necessarily limited to thedescribed features or acts described above. Rather, the describedfeatures and acts are disclosed as example forms of implementing theclaims.

Those skilled in the art will appreciate that embodiments may bepracticed in network computing environments (e.g., computing environment1000) with many types of computer system configurations, including,personal computers, desktop computers, laptop computers, messageprocessors, hand-held devices, multi-processor systems,microprocessor-based or programmable consumer electronics, network PCs,minicomputers, mainframe computers, tablets, smart phones, routers,switches, and the like. Embodiments may be practiced in distributedsystem environments where local and remote computer systems, which arelinked (either by hardwired data links, wireless data links, or by acombination of hardwired and wireless data links) through a network,both perform tasks. In a distributed system environment, program modulesmay be located in both local and remote memory storage devices. Programmodules for one entity can be located and/or run in another entitiesdata center or “in the cloud.” In this specification and in thefollowing claims, a computer system is also defined to include imagingsystems (e.g., biological analysis system 100 of FIG. 1).

In some embodiments, the biological analysis system 1100 is incommunication with a server and/or computing system 1400 via a wired,wireless, and/or cloud network 1500. For example, computing system 1400includes one or more processors 1440 and one or more hardware storagedevices 1420 storing one or more computer-executable instructions 1420A,1420B, 1420C. Additionally, or alternatively, the computing systemincludes a database 146 configures to store one or more data sets (e.g.,data type 1460A, 1460B). In some instances, computing system 1400 alsoincludes a user interface 1300B. The computing environment 1000 isconfigured such that data (e.g., photodetector signal data and/or otherdata) collected by the biological analysis system 1100 is able to bestored and/or processed via computing system 1200. Additionally, oralternatively, the data from system 1100 is pushed via the network tocomputing system 1400, wherein the data can be stored in database 1460and/or processed via processor 1440 and pushed back to the computingsystem 1200 for storage and/or further processing.

In some embodiments, the biological analysis system is configured as a“smart” device capable of automatically performing biological analysistechniques and data processing and can communicate with other computingsystems to report and/or store data automatically, including raw andprocessed runtime information, excitation light and/or emission lightwavelength and intensity, etc.

The disclosed embodiments are also directed to methods for analyzingbiological samples using a biological analysis device (e.g., system 100of FIG. 1) as described herein. In some embodiments, acomputer-implemented method for analyzing a plurality of biologicalsamples includes one or more of the following steps:

-   -   1. Detecting a plurality of sample containers (e.g., within        sample receptacles 120 of FIG. 1) removably secured in a        multi-sample loading apparatus (e.g., sample loading system 800        of FIG. 8).    -   2. In response to detecting the plurality of biological sample        containers, the computing system activating an excitation light        source, wherein: excitation light generated by the excitation        light source is directed as a plurality of excitation light        beams toward the plurality of sample containers at least by a        plurality of mirrors disposed in a staggered, diagonal pattern,        each mirror is configured to direct one excitation light beam of        the plurality of excitation light beams toward one corresponding        sample container of the plurality of sample containers, and the        excitation light is configured to cause the biological samples        stored in the plurality of biological sample containers to        produce emission radiation.    -   3. Detecting an amount of emission radiation from each of the        biological samples via a plurality of photodetectors.    -   4. Determining a concentration of one or more biological        analytes includes in each of the sample containers of the        plurality of sample containers, at least based in part on the        amount of detected emission radiation.

In some embodiments, the computing system (e.g., computing system 1200)of the biological analysis device is configured to perform one or moreof the following additional and/or alternative steps:

-   -   1. Detecting a particular arrangement of sample containers and        automatically adjusting the independently adjustable excitation        mirrors (e.g., excitation mirrors 116 of FIG. 1) to correspond        to the detected arrangement of sample containers.    -   2. Determining the concentration of the one or more biological        analytes based in part on the amount of detected emission        radiation and based in part on one or more of the following        variables: a type of assay based on the anticipated biological        analyte identity associated with the one or more biological        samples, a calculated calibration curve generated from data sets        corresponding to a standards sample set, the amount of each        sample volume stored in each sample container, assay kit lot        numbers, tags, or sample identification numbers, and/or ignoring        samples that have measurements determined to be out of range        based on a calibration curve.    -   3. Displaying the determined concentrations of biological        analyte via the user interface (UI) (e.g., UI 130 a) in a        numerical and/or graphical format.    -   4. Perform molarity and other conversions and/or calculations.    -   5. Automatically adjusting the aperture dimension of the        excitation window (e.g., excitation window 606 of FIG. 6),        emission window (e.g., emission window 710 of FIG. 7) and/or        emission aperture (e.g., emission aperture 722 of FIG. 7).    -   6. Automatically export data (e.g., determined concentrations,        analyte identities, assay identities) in various formats and/or        to another computing system (e.g., computing system 1400 of FIG.        10).

In some embodiments, the user is able to input various pieces of data asdescribed above, wherein the computing system can store and/or processthe data in addition to storing and/or processing data collected by thecomputing system via the biological analysis device.

As described, the biological analysis systems of the present disclosureare capable of simultaneously analyzing multiple samples, while having acompact form factor. Sample loading and unloading are also simplified,while ensuring that the sample containers are securely and correctlypositioned.

It will be appreciated by a person skilled in the art that numerousvariations and/or modifications may be made to the present invention asshown in the specific embodiments without departing from the scope ofthe invention as broadly described.

What is claimed is:
 1. A biological analysis system comprising: anexcitation module, comprising: a collimator element configured toreceive excitation light from at least one excitation light source andto transmit collimated excitation light along an excitation light pathin a first direction; and a plurality of excitation mirrors arrayedalong the excitation light path, wherein each excitation mirror isdisposed at an acute angle relative to the first direction andconfigured to reflect a respective beam of collimated excitation lightalong a second direction of the excitation light path; and an emissionmodule positioned to receive excitation light transmitted along thesecond direction of the excitation light path, the emission modulecomprising: a sample block comprising a plurality of sample receptacles,each sample receptacle positioned to receive a respective beam ofcollimated excitation light transmitted along the second direction ofthe excitation light path; and a plurality of photodetectors, eachphotodetector configured to receive emission light transmitted in athird direction from a respective sample receptacle, the third directionbeing transverse to the second direction of the excitation light path.2. The biological analysis system of claim 1, wherein the excitationmodule additionally comprises a plurality of excitation lenses arrayedsuch that each excitation lens is positioned in the second direction ofthe excitation light path and is configured to focus a respective,reflected beam of collimated light into a respective focused beam ofexcitation light to be received at a respective sample receptacle of theemission module.
 3. The biological analysis system of claim 2, whereineach photodetector is oriented in the third direction toward therespective sample receptacle.
 4. The biological analysis system of claim3, wherein the third direction is substantially orthogonal to the seconddirection of the excitation light path.
 5. The biological analysissystem of claim 1, wherein the emission module additionally comprises aplurality of emission lenses configured to focus emission lighttransmitted in the third direction onto the plurality of photodetectors.6. The biological analysis system of claim 5, wherein the emissionmodule additionally comprises a plurality of emission filterscorresponding to the plurality of emission lenses, the plurality ofemission filters being positioned downstream of the correspondingplurality of emission lenses and configured to allow emission light topass through the emission filter and to substantially block strayexcitation light.
 7. The biological analysis system of claim 6, whereinthe plurality of emission filters comprise dual bandpass filters.
 8. Thebiological analysis system of claim 5, wherein each emission lenscomprises a curved lens.
 9. The biological analysis system of claim 1,wherein the emission module further comprises a plurality of emissionwindows, each emission window associated with a respective samplereceptacle and defining an area through which emission light istransmitted to downstream components in the third direction.
 10. Thebiological analysis system of claim 1, wherein at least one of theplurality of excitation mirrors is independently adjustable.
 11. Thebiological analysis system of claim 1, wherein the plurality ofexcitation mirrors are arrayed in a staggered, diagonal pattern formedby a first center point of a first excitation lens being offsetvertically and horizontally from a second center point of a secondexcitation lens, and the acute angle of each excitation mirror in thestaggered, diagonal pattern is between 50° and 75° relative to the firstdirection.
 12. A biological analysis system comprising: an excitationmodule comprising: an excitation light source configured to emitexcitation light in a first direction; an excitation mirror selectivelymovable between a plurality of predefined positions, each predefinedposition forming an acute angles relative to the first direction andbeing configured to reflect the excitation light along a seconddirection; and a plurality of excitation lenses arrayed such that eachexcitation lens is positioned in the second direction and is configuredto receive a reflected beam of excitation light directed thereto by theexcitation mirror positioned in a respective predefined position; and anemission module comprising: a plurality of sample receptacles positionedto receive focused beams of reflected excitation light from thecorresponding plurality of excitation lenses; and at least onephotodetector configured to receive emission light transmitted in athird direction from the plurality of sample receptacles, the thirddirection being transverse to the second direction.
 13. The biologicalanalysis system of claim 12, wherein the emission module additionallycomprises a plurality of emission lenses and a plurality of emissionfilters configured to focus and filter the emission light onto the atleast one photodetector.
 14. The biological analysis system of claim 13,wherein the at least one photodetector comprises a plurality ofphotodetectors, each photodetector configured to receive emission lightfrom a respective sample receptacle, the emission light having beenfocused and filtered by respective emission lenses and respectiveemission filters before being received at each photodetector.
 15. Thebiological analysis system of claim 12, further comprising a sampleloading system configured to removably secure one or more samplecontainers within corresponding sample receptacles of the plurality ofsample receptacles.
 16. The biological analysis system of claim 15,wherein the sample loading system further comprises a closing mechanismconfigured to exert a closing force on—and to positionally secure—theone or more sample containers within the corresponding samplereceptacles.
 17. The biological analysis system of claim 12, wherein theemission light comprises fluorescence radiation from one or more excitedfluorescent labels.
 18. The biological analysis system of claim 13,further comprising a plurality of emission apertures, wherein eachemission aperture is associated with a respective emission lens of theplurality of emission lenses, and wherein each emission aperture isaligned in the third direction and defines an area through whichemission light is received from the sample receptacle by the respectiveemission lens.
 19. The biological analysis system of claim 18, wherein acenter point of the emission aperture is aligned with an optical centerof the respective emission lens.
 20. A biological analysis system,comprising: at least two excitation light sources emitting differentexcitation wavelengths; a collimator element configured to receiveexcitation light from the at least two excitation light sources and totransmit collimated excitation light along an excitation light path in afirst direction; a plurality of excitation mirrors arrayed in astaggered, diagonal pattern along the excitation light path, whereineach excitation mirror is disposed at an acute angle relative to thefirst direction and configured to reflect a respective beam ofcollimated excitation light along a second direction of the excitationlight path; a plurality of excitation lenses positioned in the seconddirection of the excitation light path and is configured to focusrespective, reflected beam of collimated light into correspondingfocused beams of excitation light; a sample block forming a plurality ofsample receptacles, wherein the plurality of sample receptacles arepositioned to receive the corresponding focused beams of excitationlight; and for each respective sample receptacle, the biologicalanalysis system comprises at least the following components aligned in athird direction, the third direction being transverse to the seconddirection: an emission window defining an area through which emissionlight is transmitted in the third direction; a curved lens configured tofocus the emission light passing through the emission window; a dualbandpass filter for substantially blocking stray excitation light; and aphotodetector configured to receive the focused, filtered emissionlight.